Spoilers just in case, but have the two of them had any encounters since Secret Wars/The New Universe? I haven't read many stories that had the two of them encountering one another. I do remember Doom encountering Magneto during Onslaught (Well, it was his clone Joseph, but he was thought to be the real deal at the time.), and Doom came to him saying that they've worked together in the past, but I don't recall when. They were at odds during the Fantastic Four Versus X-Men mini series in the 80's (But Mags was leading the X-Men at the time.). I know that there was a storyarc in the original Super Villain Team-Up series that had Magneto teaming up with the Beast to take down Dr. Doom. Have there been any more encounters between the two? If they were the two main villains of the MU, you think that they would work together more. Doom and Kang certainly have.
They weren't exactly at odds in FF vs X-Men. Their interaction was very minimal in that mini though. Our Lord Magneto spent most of that mini sulking.